<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div><span class="Apple-style-span" style="font-size: medium; font-family: 'Times New Roman', serif; ">correct_est_fusion is not guaranteed to never merge a gene. If you are giving maker imperfect evidence, there is only so much it can do. Also you should be using protein evidence in combination with EST evidence, especially when using the correct_est_fusion option or you are limiting it's effectiveness. MAKER does not work as well on ESTs alone, especially for organisms with few introns as internal logic is relying on the combination of evidence support.</span></div><div><span class="Apple-style-span" style="font-size: medium; font-family: 'Times New Roman', serif; "><br></span></div><div><span class="Apple-style-span" style="font-size: medium; font-family: 'Times New Roman', serif; ">--Carson</span></div><div><span class="Apple-style-span" style="font-size: medium; font-family: 'Times New Roman', serif; "><br></span></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> 刘慧泉 <<a href="mailto:liuhuiquan@nwsuaf.edu.cn">liuhuiquan@nwsuaf.edu.cn</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 16 April, 2013 9:49 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] *maker.proteins and*non_overlapping_ab_initio.proteins files<br></div><div><br></div><div><br><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">Hi Carson and Daniel,<!--?xml:namespace prefix = "o" ns = "urn:schemas-microsoft-com:office:office" /--><o:p></o:p></font></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p><font size="3"> </font></o:p></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">Thank you very much for your quick responses! <o:p></o:p></font></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p><font size="3"> </font></o:p></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">By multiple tries, I have known the reason why only a few genes were annotated by maker. This is due to turn on of the “correct_est_fusion” option. I got about 8000 transcripts from PASA assembly. Because the gene density of my fungus is very high, many of the assembled transcripts merged adjacent genes even if the trinity and PASA were used with relevant parameter. Maker may not use the merged transcripts as evidence, it the “correct_est_fusion” option is turn on. However, even though the “correct_est_fusion” option is used, I also found many genes produced by maker have merged more than one gene.<o:p></o:p></font></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p><font size="3"> </font></o:p></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">I’m now using the ORFs (trainingSetCandidates.cds) extracted from the transcripts by PASA as the EST evidence supplied to maker. I found most of the extracted ORF can accurate match the gene model predicted by augustus and genemark. This can better resolve the “merged gene” issues for fungi with high gene density.<o:p></o:p></font></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p><font size="3"> </font></o:p></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">For the 'non-overlapping' file, if only using genemark, its predictions can be found in the 'non-overlapping' file. Is previously issue due to the gene mode generated by augustus is better that genemark, so only augustus gene was putted into the 'non-overlapping' file? Will the genes predicted only by one program not found in the 'non-overlapping' file? how to get these genes?</font></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><o:p><font size="3"> </font></o:p></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">Thank you<o:p></o:p></font></span></p><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="font-family: 'Times New Roman', serif; "><font size="3">Huiquan<o:p></o:p></font></span></p><br><quark_editor_sign><br><b>发件人: </b>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><b>发送时间: </b>2013-04-16 24:01<br><b>收件人: </b>刘慧泉 <<a href="mailto:liuhuiquan@nwsuaf.edu.cn">liuhuiquan@nwsuaf.edu.cn</a>>;<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>主 题: </b>Re:Re: [maker-devel] *maker.proteins and*non_overlapping_ab_initio.proteins files<br><br><div style="FONT-SIZE: 14px; FONT-FAMILY: Calibri, sans-serif"><span class="Apple-style-span" style="FONT-SIZE: medium; FONT-FAMILY: " ?="" serif;="" roman?,="" new="" times=""><span style="mso-spacerun: yes"> </span>1. by view the gff file produced by maker2, I have found most of the predicted gene loci have est matches. but why only 254 gene annotations got by maker2 ?</span></div><div style="FONT-SIZE: 14px; FONT-FAMILY: Calibri, sans-serif"><br></div><blockquote style="BORDER-TOP: medium none; BORDER-RIGHT: medium none; BORDER-BOTTOM: medium none; PADDING-BOTTOM: 0px; PADDING-TOP: 0px; PADDING-LEFT: 0px; MARGIN: 0px 0px 0px 40px; BORDER-LEFT: medium none; PADDING-RIGHT: 0px"><blockquote style="BORDER-TOP: medium none; BORDER-RIGHT: medium none; BORDER-BOTTOM: medium none; PADDING-BOTTOM: 0px; PADDING-TOP: 0px; PADDING-LEFT: 0px; MARGIN: 0px 0px 0px 40px; BORDER-LEFT: medium none; PADDING-RIGHT: 0px"><div style="FONT-SIZE: 14px; FONT-FAMILY: Calibri, sans-serif">I'd really have to see the results to tell you why.</div></blockquote></blockquote><span id="OLK_SRC_BODY_SECTION"><div><p class="MsoNormal" style="FONT-SIZE: 14px; FONT-FAMILY: Calibri, sans-serif; MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-FAMILY: " ?="" serif;="" roman?,="" new="" times=""><font size="3"><!-- --><o:p><br><!-- --></o:p></font></span></p><p class="MsoNormal" style="FONT-SIZE: 14px; FONT-FAMILY: Calibri, sans-serif; MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 5.25pt"><span lang="EN-US" style="FONT-FAMILY: " ?="" serif;="" roman?,="" new="" times=""><font size="3">2. in the “non-overlapping ab initio”file, I found sequences are all from augustus_masked prediction. Does the non-overlapping file only include the best gene modes from predicted by both augustus and genemark? <span style="mso-spacerun: yes"> </span>Does it include genemark- or augustus-specific genes ?<o:p></o:p></font></span></p><p class="MsoNormal" style="FONT-SIZE: 14px; FONT-FAMILY: Calibri, sans-serif; MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="FONT-FAMILY: " ?="" serif;="" roman?,="" new="" times=""><o:p><font size="3"> </font></o:p></span></p><blockquote style="BORDER-TOP: medium none; BORDER-RIGHT: medium none; BORDER-BOTTOM: medium none; PADDING-BOTTOM: 0px; PADDING-TOP: 0px; PADDING-LEFT: 0px; MARGIN: 0px 0px 0px 40px; BORDER-LEFT: medium none; PADDING-RIGHT: 0px"><blockquote style="BORDER-TOP: medium none; BORDER-RIGHT: medium none; BORDER-BOTTOM: medium none; PADDING-BOTTOM: 0px; PADDING-TOP: 0px; PADDING-LEFT: 0px; MARGIN: 0px 0px 0px 40px; BORDER-LEFT: medium none; PADDING-RIGHT: 0px"><p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><font class="Apple-style-span" face="Times New Roman,serif">The 'non-overlapping' file should have the one with best consensus if there are 3 or more predictors, and the longest one otherwise. It should be able to have augustus and genemark genes. Try it with only genemark and let me know if the file is empty.</font></p></blockquote></blockquote></div></span><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div></quark_editor_sign></div>_______________________________________________
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